Atomistry » Magnesium » PDB 5gqx-5gx4 » 5gwi
Atomistry »
  Magnesium »
    PDB 5gqx-5gx4 »
      5gwi »

Magnesium in PDB 5gwi: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi was solved by Y.R.Wang, S.F.Chen, C.C.Wu, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.788, 176.966, 94.528, 90.00, 112.30, 90.00
R / Rfree (%) 21.4 / 25.3

Other elements in 5gwi:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R also contains other interesting chemical elements:

Platinum (Pt) 4 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R (pdb code 5gwi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 1 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:49.5
occ:1.00
 OD2 A:ASP559 2.4 33.5 1.0
O A:HOH1412 2.5 42.0 1.0
OD2 A:ASP557 2.6 61.8 1.0
CG A:ASP559 3.5 32.4 1.0
CG A:ASP557 3.6 56.6 1.0
OD1 A:ASP559 3.8 40.1 1.0
CB A:ASP557 3.9 46.2 1.0
OE2 A:GLU477 4.1 53.2 1.0
OP1 C:DC8 4.1 47.6 1.0
O3' C:DC8 4.3 49.1 1.0
C5' C:DC8 4.3 36.6 1.0
CD A:GLU477 4.7 56.5 1.0
CB A:ASP559 4.7 27.8 1.0
OE1 A:GLU477 4.7 58.7 1.0
OD1 A:ASP557 4.8 69.4 1.0
C4' C:DC8 5.0 39.1 1.0
O5' C:DC8 5.0 38.3 1.0

Magnesium binding site 2 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 2 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1304

b:54.9
occ:1.00
 O A:GLY868 3.2 48.5 1.0
O A:ASN867 3.2 51.6 1.0
OE1 A:GLU870 3.8 76.6 1.0
OP1 C:DG5 3.8 50.8 1.0
C A:GLY868 4.3 42.0 1.0
C A:ASN867 4.4 42.4 1.0
CG A:GLU870 4.6 43.9 1.0
CD A:GLU870 4.6 63.4 1.0
O A:HOH1443 4.7 37.8 1.0
O A:SER794 4.7 35.0 1.0
OD1 A:ASN786 4.8 33.4 1.0
OD1 A:ASN795 4.8 38.0 1.0
CA A:GLY868 4.9 39.9 1.0

Magnesium binding site 3 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 3 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:44.4
occ:1.00
 OD2 B:ASP557 2.4 54.6 1.0
O B:HOH1420 2.4 35.8 1.0
OD2 B:ASP559 2.7 35.1 1.0
O E:HOH201 2.9 35.8 1.0
CG B:ASP557 3.4 47.5 1.0
CG B:ASP559 3.7 37.0 1.0
CB B:ASP557 3.8 37.2 1.0
OD1 B:ASP559 4.0 41.9 1.0
OE1 B:GLU477 4.0 36.6 1.0
O3' E:DC8 4.2 49.1 1.0
OP1 E:DC8 4.2 27.5 1.0
C5' E:DC8 4.4 30.1 1.0
OD1 B:ASP557 4.5 76.0 1.0
CD B:GLU477 4.6 47.6 1.0
OE2 B:GLU477 4.6 45.4 1.0
O B:HOH1401 5.0 35.0 1.0
C4' E:DC8 5.0 33.5 1.0

Magnesium binding site 4 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 4 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:64.9
occ:1.00
 O D:HOH203 2.5 54.0 1.0
O D:HOH201 2.8 37.9 1.0
O B:HOH1478 3.6 43.3 1.0
O6 D:DG17 4.4 49.6 1.0
O6 D:DG18 4.5 40.6 1.0
O6 E:DG2 4.7 44.8 1.0
N7 D:DG17 4.8 34.5 1.0
N4 E:DC3 4.8 34.0 1.0

Magnesium binding site 5 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 5 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:61.8
occ:1.00
 OP1 E:DG5 3.4 46.2 1.0
O B:ASN867 3.9 42.9 1.0
OD1 B:ASN786 4.1 46.3 1.0
O B:SER794 4.2 44.9 1.0
OD1 B:ASN795 4.2 32.8 1.0
C B:SER794 4.4 35.6 1.0
ND2 B:ASN786 4.4 42.1 1.0
O B:GLY868 4.5 43.9 1.0
CA B:SER794 4.6 31.5 1.0
CG B:ASN786 4.7 51.7 1.0
CG B:ASN795 4.8 34.8 1.0
P E:DG5 4.8 49.4 1.0

Magnesium binding site 6 out of 6 in 5gwi

Go back to Magnesium Binding Sites List in 5gwi
Magnesium binding site 6 out of 6 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:59.0
occ:1.00
 N7 F:DG17 4.6 40.2 1.0
O6 F:DG17 4.6 52.3 1.0
O6 F:DG18 4.8 44.0 1.0
C5 F:DC16 4.9 32.8 1.0

Reference:

Y.R.Wang, S.F.Chen, C.C.Wu, Y.W.Liao, T.S.Lin, K.T.Liu, Y.S.Chen, T.K.Li, T.C.Chien, N.L.Chan. Producing Irreversible Topoisomerase II-Mediated Dna Breaks By Site-Specific Pt(II)-Methionine Coordination Chemistry Nucleic Acids Res. V. 45 10861 2017.
ISSN: ESSN 1362-4962
PubMed: 28977631
DOI: 10.1093/NAR/GKX742
Page generated: Mon Dec 14 20:25:36 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy